arXiv subjects

Hanchen Wang

Publications and source records attributed to Hanchen Wang.

At least 55 records · Page 3Linked to original sources

arXiv2025

3D Interaction Geometric Pre-training for Molecular Relational Learning

Molecular Relational Learning (MRL) is a rapidly growing field that focuses on understanding the interaction dynamics between molecules, which is crucial for applications ranging from catalyst engineering to drug discovery. Despite recent progress, earlier MRL approaches are limited to using only the 2D topological structure of molecules, as obtaining the 3D interaction geometry remains prohibitively expensive. This paper introduces a novel 3D geometric pre-training strategy for MRL (3DMRL) that incorporates a 3D virtual interaction environment, overcoming the limitations of costly traditional quantum mechanical calculation methods. With the constructed 3D virtual interaction environment, 3DMRL trains 2D MRL model to learn the global and local 3D geometric information of molecular interaction. Extensive experiments on various tasks using real-world datasets, including out-of-distribution and extrapolation scenarios, demonstrate the effectiveness of 3DMRL, showing up to a 24.93% improvement in performance across 40 tasks. Our code is publicly available at https://github.com/Namkyeong/3DMRL.

cs.LG↗

arXiv2025

Accelerating K-Core Computation in Temporal Graphs

We address the problem of enumerating all temporal k-cores given a query time range and a temporal graph, which suffers from poor efficiency and scalability in the state-of-the-art solution. Motivated by an existing concept called core times, we propose a novel algorithm to compute all temporal $k$-cores based on core times and prove that the algorithmic running time is bounded by the size of all resulting temporal k-cores, which is optimal in this scenario. Meanwhile, we show that the cost of computing core times is much lower, which demonstrates the close relevance between our overall running time and the result size.

cs.DB↗

arXiv2025

Observation and Control of Chiral Spin Frustration in BiYIG Thin Films

Chiral interactions within magnetic layers stabilize the formation of noncollinear spin textures, which can be leveraged to design devices with tailored magnetization dynamics. Here, we introduce chiral spin frustration in which energetically degenerate magnetic states frustrate the Dzyaloshinskii-Moriya interaction. We demonstrate magnon-driven switching of the chirally frustrated spin states in Bi-substituted yttrium iron garnet thin films. These states are defined by an in-plane macrospin neighboring two out-ofplane spins on either side with opposing chirality. Using scanning nitrogen-vacancy magnetometry and spin pumping, we identified four degenerate frustrated states and achieved their controllable switching via magnon spin torque. Crucially, the switching is unidirectional, with selectivity determined by the incoming magnon direction. This mechanism provides a powerful approach to manipulate frustrated spin states with magnons. Chiral spin frustration unlocks the geometry constraints of conventional frustration, and therefore opens new horizons for frustrated magnetism, paving the way for energy-efficient spintronic devices based on frustratio

cond-mat.mes-hall↗

arXiv2025

WOCD: A Semi-Supervised Method for Overlapping Community Detection Using Weak Cliques

Overlapping community detection (OCD) is a fundamental graph data analysis task for extracting graph patterns. Traditional OCD methods can be broadly divided into node clustering and link clustering approaches, both of which rely solely on link information to identify overlapping communities. In recent years, deep learning-based methods have made significant advancements for this task. However, existing GNN-based approaches often face difficulties in effectively integrating link, attribute, and prior information, along with challenges like limited receptive fields and over-smoothing, which hinder their performance on complex overlapping community detection. In this paper, we propose a Weak-clique based Overlapping Community Detection method, namely WOCD, which incorporates prior information and optimizes the use of link information to improve detection accuracy. Specifically, we introduce pseudo-labels within a semi-supervised framework to strengthen the generalization ability, making WOCD more versatile. Furthermore, we initialize pseudo-labels using weak cliques to fully leverage link and prior information, leading to better detection accuracy. Additionally, we employ a single-layer Graph Transformer combined with GNN, which achieves significant performance improvements while maintaining efficiency. We evaluate WOCD on eight real-world attributed datasets, and the results demonstrate that it outperforms the state-of-the-art semi-supervised OCD method by a significant margin in terms of accuracy.

cs.SI↗

arXiv2025

Lattice-tunable substituted iron garnets for low-temperature magnonics

The synthesis of nm-thick epitaxial films of iron garnets by physical vapor deposition has opened up exciting opportunities for the on-chip generation and processing of microwave signals encoded in magnons. However, iron garnet thin films suffer from demanding lattice-matching and stoichiometry requirements. Here a new approach to their synthesis is developed, enabling a precise and continuous tuning of iron garnet compositions based on the co-sputtering of binary oxides. By substituting a controlled proportion of iron with additional yttrium, Y$_{3}$(Y$_{x}$Fe$_{5-x}$)O$_{12}$ films of high crystalline quality are obtained, combining a widely tunable lattice parameter and excellent magnetization dynamics. This enables iron garnet thin films suited for cryogenic applications, which have long remained impractical due to microwave losses caused by paramagnetic garnet substrates. Low-temperature ferromagnetic resonance confirms the elimination of substrate paramagnetic losses for Y$_{3}$(Y$_{x}$Fe$_{5-x}$)O$_{12}$ films lattice-matched to Y$_{3}$Sc$_{2}$Ga$_{3}$O$_{12}$ (YSGG), a diamagnetic substrate. The Y$_{3}$(Y$_{x}$Fe$_{5-x}$)O$_{12}$ system can be matched to other substrates such as (Gd,Y)$_{3}$Sc$_{2}$Ga$_{3}$O$_{12}$. Bi-substituted films of (Bi$_{0.8}$Y$_{2.2}$)Fe$_{5}$O$_{12}$ also have ideal lattice matching to YSGG, demonstrating the versatility of this approach. This opens unprecedented options for cation substitutions in iron garnet films, offering a promising avenue to new properties and quantum magnonic devices operating in low-temperature environments.

cond-mat.mtrl-sci↗

arXiv2025

Current-Controlled Magnon-Magnon Coupling in an On-Chip Cavity Resonator

Harnessing spin currents to control magnon dynamics enables new functionalities in magnonic devices. Here, we demonstrate current-controlled magnon-magnon coupling between cavity and boundary modes in an ultrathin film of Bi-doped yttrium iron garnet (BiYIG). Cavity modes emerge in a BiYIG region between two Pt nanostripes, where interfacial anisotropy modifies the magnon dispersion. These modes hybridize with boundary magnons confined within the Pt-capped BiYIG, resulting in an anticrossing gap. Modeling based on dipole-exchange spin-wave dispersion accurately reproduces the observed modes and their hybridization. Spin current injection via the spin Hall effect in a Pt nanostripe disrupts the cavity boundary conditions and suppresses both cavity modes and hybridization upon driving the system beyond the damping compensation threshold. Furthermore, tuning the microwave power applied to a microstrip antenna enables controlled detuning of the anticrossing gap. Our findings provide a platform for exploring spin current-magnon interactions and designing on-chip reconfigurable magnonic devices.

cond-mat.mes-hall↗

arXiv2025

Orbital Pumping in Ferrimagnetic Insulators

We report the detection of pure orbital currents generated by both coherent and thermal magnons in the magnetic insulator Bi-doped yttrium iron garnet (BiYIG). The pumping of orbital and spin currents is jointly investigated in nano-devices made of naturally oxidized Cu, pure Cu, Pt, and Cr. The absence of charge conduction in BiYIG and the negligible spin-to-charge conversion of oxidized Cu allows us to disambiguate the orbital current contribution. Comparative measurements on YIG and BiYIG show that the origin of the orbital pumping in BiYIG/oxidized Cu is the dynamics of the orbital magnetization in the magnetic insulator. In Cr, the pumping signal is dominated by the negative spin Hall effect rather than the positive orbital Hall effect, indicating that orbital currents represent a minority of the total angular momentum current pumped from the magnetic insulator. Our results also evidence that improving the interfacial transparency significantly enhances pumping efficiencies not only for spin, but also for orbital currents.

cond-mat.mes-hall↗

arXiv2025

DiffGED: Computing Graph Edit Distance via Diffusion-based Graph Matching

The Graph Edit Distance (GED) problem, which aims to compute the minimum number of edit operations required to transform one graph into another, is a fundamental challenge in graph analysis with wide-ranging applications. However, due to its NP-hard nature, traditional A* approaches often suffer from scalability issue, making them computationally intractable for large graphs. Many recent deep learning frameworks address GED by formulating it as a regression task, which, while efficient, fails to recover the edit path -- a central interest in GED. Furthermore, recent hybrid approaches that combine deep learning with traditional methods to recover the edit path often yield poor solution quality. These methods also struggle to generate candidate solutions in parallel, resulting in increased running times.In this paper, we present a novel approach, DiffGED, that leverages generative diffusion model to solve GED and recover the corresponding edit path. Specifically, we first generate multiple diverse node matching matrices in parallel through a diffusion-based graph matching model. Next, node mappings are extracted from each generated matching matrices in parallel, and each extracted node mapping can be simply transformed into an edit path. Benefiting from the generative diversity provided by the diffusion model, DiffGED is less likely to fall into local sub-optimal solutions, thereby achieving superior overall solution quality close to the exact solution. Experimental results on real-world datasets demonstrate that DiffGED can generate multiple diverse edit paths with exceptionally high accuracy comparable to exact solutions while maintaining a running time shorter than most of hybrid approaches.

cs.LG↗

arXiv2025

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

cs.LG↗

arXiv2025

Controlling spin currents with magnon interference in a canted antiferromagnet

Controlling spin current lies at the heart of spintronics and its applications. The sign of spin currents is monotonous in ferromagnets once the current direction is determined. Spin currents in antiferromagnets can possess opposite polarization, but requires enormous magnetic fields to lift the degeneracy. Controlling spin currents with different polarization is urgently demanded but remains hitherto elusive. Here, we demonstrate the control of spin currents at room temperature by magnon interference in a canted antiferromagnet, hematite recently also classified as an altermagnet. Magneto-optical characterization by Brillouin light scattering revealed that the spatial periodicity of the beating patterns was tunable via the microwave frequency. The inverse spin-Hall voltage changed sign as the frequency was scanned, i.e., a frequency-controlled switching of polarization in pure spin currents was obtained. Our work marks the use of antiferromagnetic magnon interference to control spin currents, which substantially extends the horizon for the emerging field of coherent antiferromagnetic spintronics.

cond-mat.mes-hall↗

arXiv2025

AI-Empowered Catalyst Discovery: A Survey from Classical Machine Learning Approaches to Large Language Models

Catalysts are essential for accelerating chemical reactions and enhancing selectivity, which is crucial for the sustainable production of energy, materials, and bioactive compounds. Catalyst discovery is fundamental yet challenging in computational chemistry and has garnered significant attention due to the promising performance of advanced Artificial Intelligence (AI) techniques. The development of Large Language Models (LLMs) notably accelerates progress in the discovery of both homogeneous and heterogeneous catalysts, where their chemical reactions differ significantly in material phases, temperature, dynamics, etc. However, there is currently no comprehensive survey that discusses the progress and latest developments in both areas, particularly with the application of LLM techniques. To address this gap, this paper presents a thorough and systematic survey of AI-empowered catalyst discovery, employing a unified and general categorization for homogeneous and heterogeneous catalysts. We examine the progress of AI-empowered catalyst discovery, highlighting their individual advantages and disadvantages, and discuss the challenges faced in this field. Furthermore, we suggest potential directions for future research from the perspective of computer science. Our goal is to assist researchers in computational chemistry, computer science, and related fields in easily tracking the latest advancements, providing a clear overview and roadmap of this area. We also organize and make accessible relevant resources, including article lists and datasets, in an open repository at https://github.com/LuckyGirl-XU/Awesome-Artificial-Intelligence-Empowered-Catalyst-Discovery.

cs.CE↗

arXiv2025

Learned Correction Methods for Ultrasound Computed Tomography Imaging Using Simplified Physics Models

Ultrasound computed tomography (USCT) is an emerging modality for breast imaging. Image reconstruction methods that incorporate accurate wave physics produce high resolution quantitative images of acoustic properties but are computationally expensive. The use of a simplified linear model in reconstruction reduces computational expense at the cost of reduced accuracy. This work aims to systematically compare different learning approaches for USCT reconstruction utilizing simplified linear models. This work considered various learning approaches to compensate for errors stemming from a linearized wave propagation model: correction in the data and image domains. The resulting image reconstruction methods are systematically assessed, alongside data-driven and model-based methods, in four virtual imaging studies utilizing anatomically realistic numerical phantoms. Image quality was assessed utilizing relative root mean square error (RRMSE), structural similarity index measure (SSIM), and a task-based assessment for tumor detection. Correction in the measurement domain resulted in images with minor visual artifacts and highly accurate task performance. Correction in the image domain demonstrated a heavy bias on training data, resulting in hallucinations, but greater robustness to measurement noise. Combining both forms of correction performed best in terms of RRMSE and SSIM, at the cost of task performance. This work systematically assessed learned reconstruction methods incorporating an approximated physical model for USCT imaging. Results demonstrated the importance of incorporating physics, compared to data-driven methods. Learning a correction in the data domain led to better task performance and robust out-of-distribution generalization compared to correction in the image domain.

eess.IV↗

arXiv2025

RIDA: A Robust Attack Framework on Incomplete Graphs

Graph Neural Networks (GNNs) are vital in data science but are increasingly susceptible to adversarial attacks. To help researchers develop more robust GNN models, it's essential to focus on designing strong attack models as foundational benchmarks and guiding references. Among adversarial attacks, gray-box poisoning attacks are noteworthy due to their effectiveness and fewer constraints. These attacks exploit GNNs' need for retraining on updated data, thereby impacting their performance by perturbing these datasets. However, current research overlooks the real-world scenario of incomplete graphs. To address this gap, we introduce the Robust Incomplete Deep Attack Framework (RIDA). It is the first algorithm for robust gray-box poisoning attacks on incomplete graphs. The approach innovatively aggregates distant vertex information and ensures powerful data utilization. Extensive tests against 9 SOTA baselines on 3 real-world datasets demonstrate that RIDA's superiority in handling incompleteness and high attack performance on the incomplete graph.

cs.LG↗

arXiv2024

DeFault: Deep-learning-based Fault Delineation Using the IBDP Passive Seismic Data at the Decatur CO2 Storage Site

The carbon capture, utilization, and storage (CCUS) framework is an essential component in reducing greenhouse gas emissions, with its success hinging on the comprehensive knowledge of subsurface geology and geomechanics. Passive seismic event relocation and fault detection serve as indispensable tools, offering vital insights into subsurface structures and fluid migration pathways. Accurate identification and localization of seismic events, however, face significant challenges, including the necessity for high-quality seismic data and advanced computational methods. To address these challenges, we introduce a novel deep learning method, DeFault, specifically designed for passive seismic source relocation and fault delineating for passive seismic monitoring projects. By leveraging data domain-adaptation, DeFault allows us to train a neural network with labeled synthetic data and apply it directly to field data. Using DeFault, the passive seismic sources are automatically clustered based on their recording time and spatial locations, and subsequently, faults and fractures are delineated accordingly. We demonstrate the efficacy of DeFault on a field case study involving CO2 injection related microseismic data from the Decatur, Illinois area. Our approach accurately and efficiently relocated passive seismic events, identified faults and aided in the prevention of potential geological hazards. Our results highlight the potential of DeFault as a valuable tool for passive seismic monitoring, emphasizing its role in ensuring CCUS project safety. This research bolsters the understanding of subsurface characterization in CCUS, illustrating machine learning's capacity to refine these methods. Ultimately, our work bear significant implications for CCUS technology deployment, an essential strategy in combating climate change.

physics.geo-ph↗

arXiv2024

Persistent nodal magnon-photon polariton in ferromagnetic heterostructures

Exceptional points with coalescence of eigenvalues and eigenvectors are spectral singularities in the parameter space, achieving which often needs fine-tuning of parameters in quantum systems. We predict a \textit{persistent} realization of nodal magnon-photon polariton, i.e., a polariton of long wavelength without any gap splitting in a thin ferromagnetic insulator film sandwiched by two normal metals, which persistently exists when the ferromagnet is sufficiently thick $\sim 100$~nm due to the joint effect of dissipation and dissipative coupling. We perform the model calculation \textit{beyond the perturbation theory} using a classical approach, develop a quantum scheme able to account for the Ohmic dissipation, and find ultrastrong coupling with coupling strength comparable to the bare magnon frequency. Via revealing a simple conversion relation we extend this formalism to superconductors and predict the gap opened by the ultrastrong coupling strongly depends on the direction of polariton propagation. Our findings may help search for robust non-Hermitian topological phases in magnonic and spintronic devices.

cond-mat.mes-hall↗

arXiv2024

Bridging Large Language Models and Graph Structure Learning Models for Robust Representation Learning

Graph representation learning, involving both node features and graph structures, is crucial for real-world applications but often encounters pervasive noise. State-of-the-art methods typically address noise by focusing separately on node features with large language models (LLMs) and on graph structures with graph structure learning models (GSLMs). In this paper, we introduce LangGSL, a robust framework that integrates the complementary strengths of pre-trained language models and GSLMs to jointly enhance both node feature and graph structure learning. In LangGSL, we first leverage LLMs to filter noise in the raw data and extract valuable cleaned information as features, enhancing the synergy of downstream models. During the mutual learning phase in LangGSL, the core idea is to leverage the relatively small language model (LM) to process local attributes and generate reliable pseudo-labels and informative node embeddings, which are then integrated into the GSLM's prediction phase. This approach enriches the global context and enhances overall performance. Meanwhile, GSLM refines the evolving graph structure constructed from the LM's output, offering updated labels back to the LM as additional guidance, thus facilitating a more effective mutual learning process. The LM and GSLM work synergistically, complementing each other's strengths and offsetting weaknesses within a variational information-maximizing framework, resulting in enhanced node features and a more robust graph structure. Extensive experiments on diverse graph datasets of varying scales and across different task scenarios demonstrate the scalability and effectiveness of the proposed approach.

cs.LG↗

arXiv2024

Mitigation of Gilbert Damping in the CoFe/CuOx Orbital Torque System

Charge-spin interconversion processes underpin the generation of spin-orbit torques in magnetic/nonmagnetic bilayers. However, efficient sources of spin currents such as 5d metals are also efficient spin sinks, resulting in a large increase of magnetic damping. Here we show that a partially-oxidized 3d metal can generate a strong orbital torque without a significant increase in damping. Measurements of the torque efficiency ξ and Gilbert damping α in CoFe/CuOx and CoFe/Pt indicate that ξ is comparable. The increase in damping relative to a single CoFe layer is Δα<0.002 in CoFe/CuOx and Δα ~ 0.005 - 0.02 in CoFe/Pt, depending on CoFe thickness. We ascribe the nonreciprocal relationship between Δα and ξ in CoFe/CuOx to the small orbital-to-spin current ratio generated by magnetic resonance in CoFe and the lack of an efficient spin sink in CuOx. Our findings provide new perspectives on the efficient excitation of magnetization dynamics via the orbital torque.

cond-mat.mtrl-sci↗

arXiv2024

APS-USCT: Ultrasound Computed Tomography on Sparse Data via AI-Physic Synergy

Ultrasound computed tomography (USCT) is a promising technique that achieves superior medical imaging reconstruction resolution by fully leveraging waveform information, outperforming conventional ultrasound methods. Despite its advantages, high-quality USCT reconstruction relies on extensive data acquisition by a large number of transducers, leading to increased costs, computational demands, extended patient scanning times, and manufacturing complexities. To mitigate these issues, we propose a new USCT method called APS-USCT, which facilitates imaging with sparse data, substantially reducing dependence on high-cost dense data acquisition. Our APS-USCT method consists of two primary components: APS-wave and APS-FWI. The APS-wave component, an encoder-decoder system, preprocesses the waveform data, converting sparse data into dense waveforms to augment sample density prior to reconstruction. The APS-FWI component, utilizing the InversionNet, directly reconstructs the speed of sound (SOS) from the ultrasound waveform data. We further improve the model's performance by incorporating Squeeze-and-Excitation (SE) Blocks and source encoding techniques. Testing our method on a breast cancer dataset yielded promising results. It demonstrated outstanding performance with an average Structural Similarity Index (SSIM) of 0.8431. Notably, over 82% of samples achieved an SSIM above 0.8, with nearly 61% exceeding 0.85, highlighting the significant potential of our approach in improving USCT image reconstruction by efficiently utilizing sparse data.

eess.IV↗